1 Triggers and Settings

2 Import fish and manipulate data a bit

Minimum vis for fish analysis = 2-m

Kelp depths = 5 -m Fish depths = 5, 10 -m Inv depths = 5 -m

Visibility data for 2015 are fake. DI was bad and set at 1.0 m; other sites set at 3.0 m

3 FISH

3.1 Rockfish YOY

## Joining, by = "taxa"

3.2 Fish

Fish depth = 5, 10

## Joining, by = "taxa"

3.3 Fish and YOY plot

Note: I have yellowtail here, but they are not in the multivariate stuff since we reall only saw them once.

3.4 Fish and YOY facet by site x year

## Joining, by = "taxa"

## Joining, by = "taxa"

4 ALGAE

Kelp depth = 5

## `summarise()` has grouped output by 'year', 'site', 'transect', 'species', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone'. You can override using the `.groups` argument.
## Joining, by = "site"

4.1 Canopy kelp

Ole needs to check the definitions of canopy kelp here. I took this from his code, which wasn’t finished.

4.2 Caonopy kelp 5 m only

4.3 Nerocystis at Tatoosh

4.4 Nero and Macro

## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site'. You can override using the `.groups` argument.

4.5 Big three: Nero, Macro, Ptero

Plot the big 3 species: Macro, Nero, Ptero

4.5.1 Big three 5 m only

4.5.2 Big three - Coastwide

## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.

4.5.3 Coastwide 5m only

## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.

5 INVERTEBRATES

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'species', 'zone', 'area', 'taxa'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone', 'area'. You can override using the `.groups` argument.

5.1 Summed Urchins

Ole will want to clean up the figure

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'area', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.

5.2 Urchins by species

Probably worth dropping into the supplement to show that it was mostly purple urchins. Partly interesting because there is no purple urchin fishery, but there is a red one. I think.

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.

## `summarise()` has grouped output by 'taxa'. You can override using the `.groups` argument.

5.3 Seastars

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'area', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.

Ugly..no aliby..

## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.

6 COMBINED KELP - URCHIN - SEASTAR PLOTS

6.1 By site and zone

6.2 By year and zone summarized across sites

## `summarise()` has grouped output by 'year', 'zone'. You can override using the `.groups` argument.

6.3 Summarized across sites; 5 m and 10 m depths combined

## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.

6.4 Summarized across sites; 5-m depth zone only

## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.

7 Output data for multivariate statistics

7.1 Combine kelp, fish, and inverts for capscale analysis

Not yet transformed to wide format in order to retain SD & SE info upon saving out. Transform in the Multiariate analysis rmd.

Output data files to use for multivariate ordinations.

Use these files and not raw files. Kelp and invert data have been converted to density to account for different transect lengths etc.

8 Quick view of what species to include in kelp ordinations. Basically only the big three have any abundance.

8.1 Algae

## `summarise()` has grouped output by 'species'. You can override using the `.groups` argument.

8.2 Fish

Note, the y-axes are very different

## `summarise()` has grouped output by 'taxa'. You can override using the `.groups` argument.

8.2.1 NOTES

for multivariate analysis; cut and paste to that file

fish.spp = c(“OPEL”, “HEXA”, “SECA”, “SCMA” ,“SENE”, “SEME”, ‘EMBI’,‘GOBI’)

yoy.spp = c(“SECAyoy”, “SEPIyoy”, “SEMYyoy”, “SEBYTyoy”,“RYOY”)

9 SOME USEFUL TABLES

Species Common name Group Total
Artedius harringtoni scalyhead sculpin COTT 15
Aulorhynchus flavidus tubesnout AUFL 240
bait bait-sardines-anchovy BAIT 200
Chirolophis nugator mosshead warbonnet CHNU 3
Clupeidae herring BAIT 148
Cottidae sculpins COTT 7
Embiotocidae surfperches EMBI 5
Embiotoca lateralis striped surfperch EMBI 470
Enophrys bison buffalo sculpin COTT 0
Hexagrammos decagrammus kelp greenling HEXA 522
Hemilepidotus hemilepidotus red Irish lord HEXA 7
Hexagrammos lagocephalus rock greenling HEXA 5
Hexagrammos stelleri whitespotted greenling HEXA 4
Jordania zonope longfin sculpin COTT 4
Myoxocephalus polyacanthocephalus great sculpin COTT 0
Ophiodon elongatus lingcod OPEL 45
Oxylebius pictus painted greenling HEXA 7
Pholididae gunnels PHOL 1
Rhinogobiops nicholsii blackeye goby GOBI 28
Rhacochilus vacca pile perch EMBI 11
Rimicola muscarum kelp clingfish RIMU 3
Sebastes yoy rockfish yoy RYOY 199
Scorpaenichthys marmoratus cabezon SCMA 23
Sebastes mela-flav yoy yellowtail-black yoy SEBYT 3544
Sebastes caurinus copper rockfish SECA 160
Sebastes flavidus yellowtail rockfish SEFL 1
Sebastes maliger quillback rockfish SEMA 20
Sebastes melanops black rockfish SEME 1387
Sebastes mystinus blue rockfish SEMY 36
Sebastes nebulosus china rockfish SENE 17
Sebastes pinniger canary rockfish SEPI 103
Synchirus gilli manacled sculpin COTT 5
4008
fish unidentified fish UNID 1